Environmental epigenomics and disease susceptibility

Abstract

Epidemiological evidence increasingly suggests that environmental exposures early in development have a role in susceptibility to disease in later life. In addition, some of these environmental effects seem to be passed on through subsequent generations. Epigenetic modifications provide a plausible link between the environment and alterations in gene expression that might lead to disease phenotypes. An increasing body of evidence from animal studies supports the role of environmental epigenetics in disease susceptibility. Furthermore, recent studies have demonstrated for the first time that heritable environmentally induced epigenetic modifications underlie reversible transgenerational alterations in phenotype. Methods are now becoming available to investigate the relevance of these phenomena to human disease.

Figure 1. Epigenetic regulation of metastable epialleles

a | Epigenetic regulation of the agouti gene in A^vy/a mice. White-filled circles indicate unmethylated CpG sites and black-filled circles indicate methylated CpG sites. Phaeomelanin (the product of the agouti gene) is not produced from the a allele because the agouti gene is mutated (shown as a box marked with a red cross). Two potential epigenetic states of the A^vy allele can occur within cells of A^vy/a mice. The IAP (intracisternal A particle) that lies upstream of the agouti gene can remain unmethylated, allowing ectopic expression of the gene from the IAP and resulting in a yellow coat colour (top). Alternatively, the IAP can be methylated, so that the gene is expressed under its normal developmental controls, leading to a brown coat colour (bottom). If the IAP methylation event occurs later in development and does not affect all embryonic cells, the offspring will have a mottled appearance (illustrated on the right). b | Genetically identical week 15 A^vy/a mouse littermates are shown, representing five coat-colour phenotypes. Mice that are predominately yellow are also clearly more obese than the brown mice. Part b reproduced with permission from REF. © (2006) National Institute of Environmental Health Sciences.

Figure 2. Effect of maternal dietary supplementation on the phenotype and epigenotype of A^vy/a offspring

a | Dietary supplementation of female mice during pregnancy. The diets of female a/a mice are supplemented with methyl-donating substances (that is, folic acid, choline, vitamin B₁₂ and betaine) or the phytoestrogen genistein 2 weeks before mating with male A^vy/a agouti mice, and throughout pregnancy and lactation. b | Maternal dietary supplementation and coat-colour distribution in A^vy/a offspring. The coat colour is primarily yellow in the offspring that are born to unsupplemented mothers, whereas it is mainly brown in the offspring from mothers that were supplemented with methyl-donating compounds or genistein. Approximately 50% of the offspring from these matings are black (a/a) but, as they do not contain an A^vy allele, they are not shown here. c | DNA methylation and agouti gene expression. Maternal hypermethylating dietary supplementation shifts the average coat-colour distribution of the offspring to brown by causing an IAP (intracisternal A particle, shown as a green bar) upstream of the agouti gene to be more methylated on average than in offspring that are born to mothers fed an unsupplemented diet. Arrow size is directly proportional to the amount of ectopic and developmental agouti gene expression. White-filled circles indicate unmethylated CpG sites and black-filled circles indicate methylated CpG sites.

Figure 3. Epigenetic regulation of imprinted alleles

Epigenetic regulation of imprinting in the murine Igf2r (insulin-like growth factor 2 receptor). Exons 1–3 of the 48-exon Igf2r gene are shown. Igf2r is imprinted in murine peripheral tissues (shown in the upper panel), and expressed from the maternal allele but not from the paternal allele. By contrast, Igf2r is biallelically expressed in neuronal cells in the brain (shown in the lower panel). The mechanism of imprinting at this locus is complex, but involves two differentially methylated regions, DMR1 and DMR2, and the expression status of the Air antisense transcript. DMR1 is differentially methylated during early development in peripheral tissues, but not in neuronal cells. In the case of DMR2, the methylation status is inherited through the germ line. Monoallelic expression of Igf2r is not only tissue-dependent, but also species-dependent^,. See REF. for more information on the role of DNA methylation and histone modification in regulating Igf2r expression in mice and humans. White-filled circles indicate unmethylated CpG sites and black-filled circles indicate methylated CpG sites.

Figure 4. Alterations in methylation status during development

During embryonic development and gonadal sex determination, primordial germ cells undergo genome-wide demethylation, which erases previous parental-specific methylation marks that regulate imprinted gene expression. In the male (coloured purple) germ line, paternal methylation marks in imprinted genes are laid down in developing gonocytes that will develop into spermatogonia. The female (coloured pink) germ line establishes maternal methylation marks in imprinted genes at a later stage. After fertilization, the paternal genome is actively demethylated (indicated by the lighter purple line in the graph), whereas the maternal genome undergoes passive demethylation (indicated by the lighter pink line in the graph). Genome-wide remethylation occurs on both parental genomes before implantation. However, imprinted genes maintain their methylation marks throughout this reprogramming, allowing for the inheritance of parental-specific monoallelic expression in somatic tissues throughout adulthood.

Figure 5. Germline transmission of epigenetically regulated transgenerational phenotypes

In a gestating mother, there is multiple-generation exposure of the F₀ female, the F₁ embryo and the F₂ generation germ line to environmental factors. The transgenerational transmission of disease phenotypes through the male germ line (labelled red) is indicated. Both male and female offspring develop disease, but the transgenerational phenotype is transmitted only paternally after exposure to vinclozolin.

Figure 6. A model for endocrine-disruptor-induced epigenetic transgenerational disease

Endocrine-disruptor action reprogrammes the epigenome of the developing germ cell during embryonic sex determination, leading to genes and other DNA sequences with altered DNA methylation. These changes are proposed to alter the transcriptomes of the testis and other organs, thereby promoting adult pathologies, some of which are inherited transgenerationally. Epigenetic mechanisms might therefore have a role in the induction of adult-onset disease through environmental exposures early in development.